Effectiveness of molecular markers for improving grain quality in Iranian rice

Document Type : Original research paper


1 Department of Agricultural Biotechnology, College of Agriculture, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran

2 Rice Research Institute of Iran-Deputy of Mazandaran, Agricultural Research, Education and Extension Organization, Amol, Iran

3 Department of Agricultural Biotechnology, College of Agriculture, Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran.


Grain and cooking qualities in rice are measured by several physical and chemical traits, each of them controlled by several genes. Molecular markers have become fast and reliable tools for screening genotypes for grain quality. However, As different populations may carrydifferent genes, the efficacy of previously developed markers in new populations should be tested. In order to assess the effectiveness of molecular markers in predicting grain quality in Iranian rice genotypes, a total of 38 genotypes from three different backgrounds were fingerprinted by 9 grain quality specific molecular markers and 10 laboratory traits.A total of 31 alleles were detected with an average of 3.1 alleles per locus and the polymorphic information content values ranged from 0.245 to 0.74. Cluster analysis based on molecular markers divided the rice genotypes into three major clusters and effectively differentiated between various genotypes. However, the dendrogram based on the common set of qualitative traits didn't succeed in discriminating between original groups. There were significant associations between molecular markers and quality traits except for milling factor. However, these associations weren't necessarility specific to their supposed traits. Therefore, association of markers developed in other rice populations, specially those developed in Japonioca populations should be tested prior to application in Iranian rice marker assisted breeding programs. 


[1]   Dela Cruz, N. and Khush, G.S. 2000. Rice grain quality evaluation procedures. In: Aromatic rices (eds. Singh, R.K., Singh, U.S., Khush, G.S), pp.15-28. New Delhi, India : Mohan Primlani
[2]     McKenzie, K.S. and Rutger, J.N. 1983. Genetic analysis of amylose content, alkali spreading score, and grain dimensions in rice. Crop Sci, 23: 306-313.
[3]     Singh, R.K., Singh, U.S., Khush, G.S., Rashmi, R. 2000. Genetics and biotechnology of quality traits in aromatic rices. In Aromatic Rices. New Delhi: Oxford & IBH Publishing Co. Pvt. Ltd., p 47.
[4]     Zhou, P. H., Tan, Y. F., He, Y. Q., Xu, C. G., Zhang, Q. 2003. Simultaneous improvement for four quality traits of Zhenshan 97, an elite parent of hybrid rice, by molecular marker-assisted selection. Theor Appl Genet, 106: 326–331.
[5]Hirose, T. and Terao, T. 2004. A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.). Planta, 220: 9-16.
[6]     Fan, C.C., Yu, X.Q., Xing, Y.Z., Xu, C.G., Luo, L.J., Zhang Q. 2005. The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population. Theor Appl Genet, 110: 1445-1452.
[7]   Waters, D.L., Henry, R.J., Reinke, R.F., Fitzgerald, M.A. 2006. Gelatinization temperature of rice explained by polymorphisms in starch synthase. Plant Biotecnol J , 4: 115-122.
[8]     Ahn, S.N., Bollich, C.N., Tanksley, S.D. 1992 . RFLP tagging of a gene for aroma in rice. Theor Appl Genet, 84: 825-828.
[9]     Lorieux, M., Petrov, M., Huang, N., Guiderdoni, E. and Ghesquiere, A. 1996. Aroma in rice: Genetic analysis of a quantitative trait. Theor Appl Genet, 93: 1145–1151.
[10]  Qiu, X., Pang, Y., Yuan, Z., Xing, D., Xu, J., Dingkuhn, M., Li, Z., Ye, G. 2015. Genome-wide association study of grain appearance and milling quality in a worldwide collection of Indica rice germplasm. PLoS ONE, 10: 12, e0145577.
[11]  Fan, C., Xing, Y., Mao, H., Lu, T., Han, B., Xu, C., Zhang, Q. 2006. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet, 112: 1164-1171.
[12]  Tan, Y.F., Xing, Y.Z., Li, J.X., Yu, S.B., Xu, C.G., Zhang, Q.F.2000. Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid. Theor Appl Genet, 101: 823–829.
[13]  Kunze, O.R. 1979. Fissuring of the rice grain after heated air-drying. Trans ASAE, 22: 1197-1202.
[14]  Amarawathi, Y., Singh, R., Singh, A.K., Singh, V.P., Mahopatra, T., Sharma, T.R., Singh, N.K. 2008. Mapping of quantitative trait loci for Basmati quality traits in rice (Oryza sativa L.). Mol Breed, 21: 49–65.
[15]  Bradbury, L., Fitzgerald, T., Henry, R., Jin, Q., Waters, D. 2005. The gene for fragrance in rice. Plant Biotechnol J, 3: 363–70.
[16]  Widjaja, R., Craske, J.D., Wootton, M. 1996. Comparative studies on volatile components of non-fragrant and fragrant rices. J Sci Food Agric, 70: 151-161
[17]  Juliano, B.O. 1971. A simplified assay for milled-rice amylose. Cereal Sci Today, 16: 334-340.
[18]  Little, R.R., Hilder, G.B., Dawson, E.H. 1958. Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chem, 35: 111-126.
[19]  Cagampang, G.B., Perez, C.M., Juliano, B.O. 1973. A gel consistency test for eating quality of rice. J Sci Food Agric, 24: 1589-1594.
[20] Juliano, B.O. and Perez, C.M. 1984. Results of a collaborative test on the measurement of grain elongation of milled rice during cooking. J Cereal Sci, 2: 281–292.
[21] He, P., Li, S.G., Qian, Q., Ma, Y.Q., Li, J.Z., Wang, W.M., Chen. Y., Zhu, L.H. 1999. Genetic analysis of rice grain quality. Theor Appl Genet, 98: 502–508.
[22]  Velupillai, L., Pandey, J.P. 1990. The impact of fissured rice on mill yields. Cereal Chem, 67: 118-124.
[23] SPSS Statistics for Windows, version 18.0 (SPSS Inc., Chicago, Ill., USA).
[24]  Rohlf, F.J. 1989. NTSYS-pc: Numerical Taxonomy and Multivariable Analysis System. Stony Brooks: State University of New York.
[25]  Ni, J., Colowit, P.M., Mackill, D.J. 2002. Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Sci, 42: 601-607.
[26]  Lee, K.J., Lee, G.A., Lee, J.R., Raveendar, S., Cho, Y.H., Lee, S.Y., Chung, J.W., Ma, K. H. 2016. Comparison of eating quality and seed storage protein among Korean rice landraces. Crop Sci Biotech, 19: 241-247.
[27]  Graham-Acquaah, S., Saito, K., Traore, K., Dieng, I., Alognon, A., Bah, S., Manful, J. T. 2018. Variations in agronomic and grain quality traits of rice grown under irrigated lowland conditions in West Africa. Food Sci Nutr, 6: 970–982.
[28]  Nakamura, Y.,Sakurai, A.,Inaba, Y.,Kimura, K., Iwasawa, N., NagamineT. 2002. The fine structure of amylopectin in endosperm fromAsian cultivated rice can be largely classified into two classes. Starch/Starke, 54: 117-131.
[29]  Zhang, Q., Yang, W., Sun, Z. 2005. Mechanical properties of sound and fissured rice kernels and their implications for rice breakage. J Food Eng, 68: 65-72.
[30]  Cnossen, A.G, & Siebenmorgen, T.J. 2000. The glass transition temperature concept in rice drying and tempering: Effect on milling quality. Trans ASAE, 43: 1661–1667.
[31]  Mapiemfu, D. L., Ndindeng, S. A., Ambang, Z., Tang, E. N., Ngome, F., Johnson, J. M., Saito, K. 2017. Physical rice grain quality as affected by biophysical factors and pre‐harvest practices. Int J Plant Prod, 11: 561– 576.
[32]  Yan, C.J., Tian, Z.X., Fang, Y.W., Yang, Y.C., Li, J., Zeng, S.Y., Gu, S.L., Xu, C.W., Tang, S. Z., Gu, M .H. 2011. Genetic analysis of starch paste viscosity parameters in glutinous rice (Oryza sativa L.). Theor Appl Genet, 122: 63–76.
[33]  Talukdar, R.P., Rathi, S., Pathak, K.H., Chetia, S.K., Sarma, R. N. 2017. Population structure and marker-trait association in indigenous aromatic rice. Rice Sci, 24: 145-154.
[34]  Nachimuthu, V.V., Muthurajan, R., Duraialaguraja, S., Sivakami, R., Pandian, B.A., Ponniah, G., Gunasekaran, K., Swaminathan, M., Suji, K.K., Sabariappan, R. 2015. Analysis of population structure and genetic diversity in rice germplasm using ssr markers: an initiative towards association mapping of agronomic traits in Oryza sativa. Rice, 8: 30.
[35]              Babu, B.K., Meena, V., Agarwal ,V., Agrawal, P.K. 2014. Population structure and genetic diversity analysis of Indian and exotic rice (Oryza sativa L.) accessions using SSR markers. Mol Biol Rep, 41: 4329-4339.
Volume 7, Issue 1
June 2019
Pages 22-30
  • Receive Date: 18 July 2019
  • Revise Date: 12 December 2019
  • Accept Date: 31 December 2019
  • First Publish Date: 31 December 2019